Depends on what information you want to parse out.... do you need the
actual alignment? If no -> use -m 8 or -m 9 and you will have a
tabular output that is easy to parse even without bioperl.
On Oct 2, 2009, at 9:29 AM, Ben Busby wrote:
> Pardon the simple question, as I am new-ish to Perl, Bioperl, and
> Computational Biology..
> I am doing a whole bunch of large BLAST searches and am wondering
> what the
> best command line BLAST commands are to put the output in a format
> best
> parsable by Bio::SearchIO.
>> Thanks!
>> Ben
>>>> --
> Economically, nothing is ever "extended by popular demand".
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--
Jason Stajich
jason.stajich at gmail.comjason at bioperl.org